DNA-based systems have been developed that are capable of performing sophisticated functions initiated by molecular recognition. Key examples are the DNA walkers where directional motion or load pick-up, transfer, and release are achieved with molecular and spatial selectivity (Gu et al., 2010; Lund et al., 2010). However, attempts to develop autonomous DNA self-replicating systems without specific sequence requirements have in recent years lagged behind (Lincoln, 2009; Patzke et al., 2007; Ye et al., 2000; Zielinkski et al., 1987). As one of the hallmarks of organisms is their ability to amplify information and materials through biocatalysis and self-replication, the development of truly biomimetic systems capable of integrated functions requires incorporating amplification into self-assembly and nanotechnology (Aldaye et al., 2008; Patzke et al., 2007; Paul et al., 2004). Replicating DNA systems not only provide tools for DNA-based nanotechnology and insights into the origins of life, but also can be used to isothermally amplify signal in DNA detection, which can simplify the requirements for point-of-care diagnostics (Aldaye et al., 2008; Connolly et al., 2010; Orgel, 1992; Patzke et al., 2007; Paul et al., 2004).
One method for introducing amplification into DNA-based systems involves generating turnover in DNA-templated processes (Grossman et al., 2008). To achieve turnover, the DNA template that facilitates the reaction of two complementary fragment strands (FIG. 1, steps A-B) must dissociate from the product after it has formed (FIG. 1, step C). However, for ligation reactions, turnover is minimal under isothermal conditions owing to the enhanced affinity of the template for the ligated product (Grossman et al., 2008). Many detection strategies have thus focused on template-triggered scission and transfer reactions rather than ligations to avoid this product inhibition (Grossman et al., 2008). One strategy for introducing turnover into ligation reactions exploits the sensitivity of DNA to destabilizing modifications present in the middle of a duplex (Silverman et al., 2006; Ye et al., 2000; Zhan et al., 1997). By ligating strands at a destabilizing site, the stability of the hybridization complex can be modified without changing the temperature or any other reaction condition (Li et al., 2003). If the stabilities of the complexes before and after ligation are properly balanced, isothermal turnover should be achieved.